Package: CAESAR.Suite Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘STMOB.Rmd’ using rmarkdown trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/MOB_ST.rda?raw=true' Content type 'application/octet-stream' length 5988380 bytes (5.7 MB) ================================================== downloaded 5.7 MB trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/MOB_scRNA.rda?raw=true' Content type 'application/octet-stream' length 48066404 bytes (45.8 MB) ================================================== downloaded 45.8 MB Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Progress: ───────────────────────────────────── 100% Progress: ────────────────────────────────────────────────── 100% Progress: ───────────────────────────────────────────────────────── 100% Progress: ──────────────────────────────────────────────────────────── 100% Progress: ────────────────────────────────────────────────────────────── 100% Progress: ─────────────────────────────────────────────────────────────── 100% Progress: ─────────────────────────────────────────────────────────────── 100% Progress: ──────────────────────────────────────────────────────────────── 100%** Processing: /home/hornik/tmp/CRAN_recheck/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-12-1.png 844x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 126860 bytes Input file size = 127118 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 96729 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 96729 Output IDAT size = 96729 bytes (30131 bytes decrease) Output file size = 96807 bytes (30311 bytes = 23.84% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-13-1.png 844x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 128341 bytes Input file size = 128599 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 97991 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 97991 Output IDAT size = 97991 bytes (30350 bytes decrease) Output file size = 98069 bytes (30530 bytes = 23.74% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-14-1.png 844x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 128341 bytes Input file size = 128599 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 97991 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 97991 Output IDAT size = 97991 bytes (30350 bytes decrease) Output file size = 98069 bytes (30530 bytes = 23.74% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-15-1.png 844x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 92821 bytes Input file size = 93031 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 68226 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 68226 Output IDAT size = 68226 bytes (24595 bytes decrease) Output file size = 68304 bytes (24727 bytes = 26.58% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-16-1.png 844x864 pixels, 3x8 bits/pixel, RGB Input IDAT size = 189490 bytes Input file size = 189844 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 170046 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 170046 Output IDAT size = 170046 bytes (19444 bytes decrease) Output file size = 170124 bytes (19720 bytes = 10.39% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-19-1.png 844x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 49756 bytes Input file size = 49906 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41497 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41497 Output IDAT size = 41497 bytes (8259 bytes decrease) Output file size = 41575 bytes (8331 bytes = 16.69% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-20-1.png 844x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 63220 bytes Input file size = 63382 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 49156 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 49156 Output IDAT size = 49156 bytes (14064 bytes decrease) Output file size = 49234 bytes (14148 bytes = 22.32% decrease) --- finished re-building ‘STMOB.Rmd’ --- re-building ‘XeniumBC.Rmd’ using rmarkdown trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/BC_scRNAList.rda?raw=true' Content type 'application/octet-stream' length 2310272 bytes (2.2 MB) ================================================== downloaded 2.2 MB trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/BC_XeniumList.rda?raw=true' Content type 'application/octet-stream' length 1256437 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/BC_feature_imgList.rda?raw=true' Content type 'application/octet-stream' length 12559173 bytes (12.0 MB) ================================================== downloaded 12.0 MB Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Progress: ─────────── 100% Progress: ───────────────── 100% Progress: ─────────────────────── 100% Progress: ────────────────────────────── 100% Progress: ─────────────────────────────────── 100% Progress: ─────────────────────────────────────────── 100% Progress: ─────────────────────────────────────────────────── 100% Progress: ─────────────────────────────────────────────────────────── 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──────────────────────────────────────────────────────────────── 100%** Processing: /home/hornik/tmp/CRAN_recheck/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/XeniumBC_files/figure-html/unnamed-chunk-12-1.png 1152x1512 pixels, 3x8 bits/pixel, RGB Input IDAT size = 529798 bytes Input file size = 530644 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 381671 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 381671 Output IDAT size = 381671 bytes (148127 bytes decrease) Output file size = 381749 bytes (148895 bytes = 28.06% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/XeniumBC_files/figure-html/unnamed-chunk-13-1.png 1152x1512 pixels, 3x8 bits/pixel, RGB Input IDAT size = 407870 bytes Input file size = 408536 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 290562 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 290562 Output IDAT size = 290562 bytes (117308 bytes decrease) Output file size = 290640 bytes (117896 bytes = 28.86% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/XeniumBC_files/figure-html/unnamed-chunk-16-1.png 1152x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 138203 bytes Input file size = 138473 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 113268 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 113268 Output IDAT size = 113268 bytes (24935 bytes decrease) Output file size = 113346 bytes (25127 bytes = 18.15% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/XeniumBC_files/figure-html/unnamed-chunk-17-1.png 1152x1512 pixels, 3x8 bits/pixel, RGB Input IDAT size = 303779 bytes Input file size = 304301 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 230022 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 230022 Output IDAT size = 230022 bytes (73757 bytes decrease) Output file size = 230100 bytes (74201 bytes = 24.38% decrease) Quitting from lines 311-319 [unnamed-chunk-18] (XeniumBC.Rmd) Error: processing vignette 'XeniumBC.Rmd' failed with diagnostics: Please run the following command to install the 'msigdbdf' package: install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev') --- failed re-building ‘XeniumBC.Rmd’ SUMMARY: processing the following file failed: ‘XeniumBC.Rmd’ Error: Vignette re-building failed. Execution halted Package: GeneNMF Check: examples New result: ERROR Running examples in ‘GeneNMF-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: runGSEA > ### Title: Run Gene set enrichment analysis > ### Aliases: runGSEA > > ### ** Examples > > data(sampleObj) > geneset <- c("BANK1","CD22","CD79A","CD19","IGHD","IGHG3","IGHM") > #test is conditional on availability of suggested packages > if (requireNamespace("fgsea", quietly=TRUE) & + requireNamespace("msigdbr", quietly=TRUE)) { + gsea_res <- runGSEA(geneset, + universe=rownames(sampleObj), + category = "C8") + } The 'msigdbdf' package must be installed to access all the data. Error in msigdbr_check_data() : Please run the following command to install the 'msigdbdf' package: install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev') Calls: runGSEA -> -> msigdbr_check_data Execution halted Package: hacksig Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘hacksig.Rmd’ using rmarkdown Quitting from lines 97-104 [unnamed-chunk-8] (hacksig.Rmd) Error: processing vignette 'hacksig.Rmd' failed with diagnostics: Please run the following command to install the 'msigdbdf' package: install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev') --- failed re-building ‘hacksig.Rmd’ SUMMARY: processing the following file failed: ‘hacksig.Rmd’ Error: Vignette re-building failed. Execution halted Package: massiveGST Check: examples New result: ERROR Running examples in ‘massiveGST-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: cut_by_NES > ### Title: Trim the table of results. > ### Aliases: cut_by_NES > > ### ** Examples > > library(massiveGST) > > # get the gene profile > fname <- system.file("extdata", package="massiveGST") > fname <- file.path(fname, "pre_ranked_list.txt") > geneProfile <- get_geneProfile(fname) > > # get the gene-sets > geneSets <- get_geneSets_from_msigdbr(category = "H", what = "gene_symbol") msigdbr: R package version 10.0.0 The 'msigdbdf' package must be installed to access all the data. Error in msigdbr_check_data() : Please run the following command to install the 'msigdbdf' package: install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev') Calls: get_geneSets_from_msigdbr -> msigdbr -> msigdbr_check_data Execution halted Package: massiveGST Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘vignette.Rmd’ using rmarkdown Quitting from lines 61-64 [unnamed-chunk-4] (vignette.Rmd) Error: processing vignette 'vignette.Rmd' failed with diagnostics: Please run the following command to install the 'msigdbdf' package: install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev') --- failed re-building ‘vignette.Rmd’ SUMMARY: processing the following file failed: ‘vignette.Rmd’ Error: Vignette re-building failed. Execution halted Package: pathfindR Check: Rd cross-references New result: WARNING Missing link(s) in Rd file 'get_gene_sets_list.Rd': ‘[msigdbr]{msigdbr_show_species}’ Missing link(s) in Rd file 'get_mgsigdb_gsets.Rd': ‘[msigdbr]{msigdbr_show_species}’ See section 'Cross-references' in the 'Writing R Extensions' manual. Package: pathfindR Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘comparing_results.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/pathfindR.Rcheck/vign_test/pathfindR/vignettes/comparing_results_files/figure-html/compare_graph1-1.png 768x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 197909 bytes Input file size = 198275 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 150954 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 150954 Output IDAT size = 150954 bytes (46955 bytes decrease) Output file size = 151032 bytes (47243 bytes = 23.83% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/pathfindR.Rcheck/vign_test/pathfindR/vignettes/comparing_results_files/figure-html/compare_graph2-1.png 768x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 55034 bytes Input file size = 55184 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 43496 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 43496 Output IDAT size = 43496 bytes (11538 bytes decrease) Output file size = 43574 bytes (11610 bytes = 21.04% decrease) --- finished re-building ‘comparing_results.Rmd’ --- re-building ‘intro_vignette.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/pathfindR.Rcheck/vign_test/pathfindR/vignettes/intro_vignette_files/figure-html/hierarchical2-1.png 672x672 pixels, 3x8 bits/pixel, RGB Input IDAT size = 50619 bytes Input file size = 50769 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 37979 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 37979 Output IDAT size = 37979 bytes (12640 bytes decrease) Output file size = 38057 bytes (12712 bytes = 25.04% decrease) --- finished re-building ‘intro_vignette.Rmd’ --- re-building ‘manual_execution.Rmd’ using rmarkdown --- finished re-building ‘manual_execution.Rmd’ --- re-building ‘non_hs_analysis.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/pathfindR.Rcheck/vign_test/pathfindR/vignettes/non_hs_analysis_files/figure-html/enr_chart-1.png 672x672 pixels, 3x8 bits/pixel, RGB Input IDAT size = 42003 bytes Input file size = 42141 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33631 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33631 Output IDAT size = 33631 bytes (8372 bytes decrease) Output file size = 33709 bytes (8432 bytes = 20.01% decrease) --- finished re-building ‘non_hs_analysis.Rmd’ --- re-building ‘obtain_data.Rmd’ using rmarkdown Quitting from lines 104-106 [unnamed-chunk-10] (obtain_data.Rmd) Error: processing vignette 'obtain_data.Rmd' failed with diagnostics: 'msigdbr_show_species' is not an exported object from 'namespace:msigdbr' --- failed re-building ‘obtain_data.Rmd’ --- re-building ‘visualization_vignette.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/pathfindR.Rcheck/vign_test/pathfindR/vignettes/visualization_vignette_files/figure-html/enr_chart3-1.png 768x768 pixels, 3x8 bits/pixel, RGB Input IDAT size = 146685 bytes Input file size = 146967 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 107961 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 107961 Output IDAT size = 107961 bytes (38724 bytes decrease) Output file size = 108039 bytes (38928 bytes = 26.49% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/pathfindR.Rcheck/vign_test/pathfindR/vignettes/visualization_vignette_files/figure-html/hmap-1.png 768x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 46166 bytes Input file size = 46304 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33875 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33875 Output IDAT size = 33875 bytes (12291 bytes decrease) Output file size = 33953 bytes (12351 bytes = 26.67% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/pathfindR.Rcheck/vign_test/pathfindR/vignettes/visualization_vignette_files/figure-html/term_gene1-1.png 768x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 109915 bytes Input file size = 110149 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 84198 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 84198 Output IDAT size = 84198 bytes (25717 bytes decrease) Output file size = 84276 bytes (25873 bytes = 23.49% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/pathfindR.Rcheck/vign_test/pathfindR/vignettes/visualization_vignette_files/figure-html/upset1-1.png 768x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 71443 bytes Input file size = 71617 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 54696 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 54696 Output IDAT size = 54696 bytes (16747 bytes decrease) Output file size = 54774 bytes (16843 bytes = 23.52% decrease) --- finished re-building ‘visualization_vignette.Rmd’ SUMMARY: processing the following file failed: ‘obtain_data.Rmd’ Error: Vignette re-building failed. Execution halted Package: RVA Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘RVA.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/RVA.Rcheck/vign_test/RVA/vignettes/RVA_files/figure-html/unnamed-chunk-10-1.png 576x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 28712 bytes Input file size = 28826 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23196 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23196 Output IDAT size = 23196 bytes (5516 bytes decrease) Output file size = 23274 bytes (5552 bytes = 19.26% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/RVA.Rcheck/vign_test/RVA/vignettes/RVA_files/figure-html/unnamed-chunk-16-1.png 576x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 42911 bytes Input file size = 43049 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32355 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32355 Output IDAT size = 32355 bytes (10556 bytes decrease) Output file size = 32433 bytes (10616 bytes = 24.66% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/RVA.Rcheck/vign_test/RVA/vignettes/RVA_files/figure-html/unnamed-chunk-19-1.png 576x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 24962 bytes Input file size = 25076 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21638 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21638 Output IDAT size = 21638 bytes (3324 bytes decrease) Output file size = 21716 bytes (3360 bytes = 13.40% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/RVA.Rcheck/vign_test/RVA/vignettes/RVA_files/figure-html/unnamed-chunk-22-1.png 576x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 31411 bytes Input file size = 31525 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26235 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26235 Output IDAT size = 26235 bytes (5176 bytes decrease) Output file size = 26313 bytes (5212 bytes = 16.53% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/RVA.Rcheck/vign_test/RVA/vignettes/RVA_files/figure-html/unnamed-chunk-26-1.png 576x384 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 13539 bytes Input file size = 14406 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12168 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12168 Output IDAT size = 12168 bytes (1371 bytes decrease) Output file size = 12246 bytes (2160 bytes = 14.99% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/RVA.Rcheck/vign_test/RVA/vignettes/RVA_files/figure-html/unnamed-chunk-27-1.png 576x384 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 15468 bytes Input file size = 16338 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13964 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13964 Output IDAT size = 13964 bytes (1504 bytes decrease) Output file size = 14042 bytes (2296 bytes = 14.05% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/RVA.Rcheck/vign_test/RVA/vignettes/RVA_files/figure-html/unnamed-chunk-31-1.png 576x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 48069 bytes Input file size = 48207 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39550 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39550 Output IDAT size = 39550 bytes (8519 bytes decrease) Output file size = 39628 bytes (8579 bytes = 17.80% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/RVA.Rcheck/vign_test/RVA/vignettes/RVA_files/figure-html/unnamed-chunk-32-1.png 576x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 53945 bytes Input file size = 54095 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 44501 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 44501 Output IDAT size = 44501 bytes (9444 bytes decrease) Output file size = 44579 bytes (9516 bytes = 17.59% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/RVA.Rcheck/vign_test/RVA/vignettes/RVA_files/figure-html/unnamed-chunk-33-1.png 576x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 28416 bytes Input file size = 28530 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21824 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21824 Output IDAT size = 21824 bytes (6592 bytes decrease) Output file size = 21902 bytes (6628 bytes = 23.23% decrease) Quitting from lines 497-498 [unnamed-chunk-37] (RVA.Rmd) Error: processing vignette 'RVA.Rmd' failed with diagnostics: Please run the following command to install the 'msigdbdf' package: install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev') --- failed re-building ‘RVA.Rmd’ SUMMARY: processing the following file failed: ‘RVA.Rmd’ Error: Vignette re-building failed. Execution halted Package: scITD Check: examples New result: ERROR Running examples in ‘scITD-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: run_gsea_one_factor > ### Title: Run gsea separately for all cell types of one specified factor > ### and plot results > ### Aliases: run_gsea_one_factor > > ### ** Examples > > test_container <- run_gsea_one_factor(test_container, factor_select=1, + method="fgsea", thresh=0.05, db_use="Hallmark", signed=TRUE) The 'msigdbdf' package must be installed to access all the data. Error in msigdbr_check_data() : Please run the following command to install the 'msigdbdf' package: install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev') Calls: run_gsea_one_factor ... rbind -> rbind -> -> msigdbr_check_data Execution halted